Client Mutation Not Found for codegen

**Intended outcome:**

I have a the following schema defined.

```
type Entity {
...
id: ID!
name: String
org: Org
...
}

input EntityInput {
name: String!
orgId: ID!
}

type Mutation {
...
CreateEntity(input: EntityInput!): Entity
...
}
```
I'm trying to create a client-side mutation and would like to get the types generated for the following mutation and returned object code.
```
mutation ClientCreateEntity(input: EntityInput!) {
CreateEntity(input: $input) {
id
name
}
}
```

I expect codegen to create the appropriate typescript models.

However, If I change the client mutation to the following:

```
mutation ClientCreateEntity {
CreateEntity(input: {name: "", orgId: ""}) {
id
name
}
}
```

It will generate typescript models.

I'm using the following cmd:

`apollo client:codegen --target typescript --config apollo.config.js --outputFlat src/specs/gen`

with the following config
```
module.exports = {
client: {
service: {
name: 'local',
url: 'http://localhost:3000/graphql',
includes: ['src/**/*.graphql'],
},
}
}
```

**Actual outcome:**

```
✔ Loading Apollo Project
✖ Generating query files with 'typescript' target
→ No operations or fragments found to generate code for.
```

**How to reproduce the issue:**

TBD. If needed I'll provide a repo repo.

**Versions**

I've tested the failing case above with the following version of the apollo package:
2.1 - 2.12, 2.19, 2.25 and 2.27.

Start with the Apollo CLI command and apollo.config.js, then inspect the operation matching files under src/**/*.graphql. Reproduce the variable-based mutation failure and compare it with the inline-input version; done means the former is discovered and TypeScript models are generated without the “No operations or fragments” error.

Written by the indexing model from the issue text.